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Update CV mappings for new instruments
Added new instrument CV mappings and detector assignments to follow PSI-MS 4.1.204
1 parent 5bac912 commit 791bd0e

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2 files changed

+158
-8
lines changed

2 files changed

+158
-8
lines changed

‎Writer/MzMlSpectrumWriter.cs‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -115,7 +115,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
115115
URI = @"https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo",
116116
fullName = "Mass spectrometry ontology",
117117
id = "MS",
118-
version = "4.1.79"
118+
version = "4.1.204"
119119
});
120120
Serialize(serializer, new CVType
121121
{

‎Writer/OntologyMapping.cs‎

Lines changed: 157 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -400,6 +400,24 @@ public static class OntologyMapping
400400
value = ""
401401
}
402402
},
403+
{
404+
"MALDI LTQ ORBITRAP XL", new CVParamType
405+
{
406+
accession = "MS:1003496",
407+
name = "MALDI LTQ Orbitrap XL",
408+
cvRef = "MS",
409+
value = ""
410+
}
411+
},
412+
{
413+
"MALDI LTQ ORBITRAP DISCOVERY", new CVParamType
414+
{
415+
accession = "MS:1003497",
416+
name = "MALDI LTQ Orbitrap Discovery",
417+
cvRef = "MS",
418+
value = ""
419+
}
420+
},
403421
{
404422
"LTQ ORBITRAP VELOS", new CVParamType
405423
{
@@ -409,6 +427,15 @@ public static class OntologyMapping
409427
value = ""
410428
}
411429
},
430+
{
431+
"LTQ ORBITRAP VELOS/ETD", new CVParamType
432+
{
433+
accession = "MS:1003499",
434+
name = "LTQ Orbitrap Velos/ETD",
435+
cvRef = "MS",
436+
value = ""
437+
}
438+
},
412439
{
413440
"ORBITRAP VELOS", new CVParamType
414441
{
@@ -422,7 +449,7 @@ public static class OntologyMapping
422449
"LTQ ORBITRAP VELOS PRO", new CVParamType
423450
{
424451
accession = "MS:1003096",
425-
name = "LTQ Orbitrap Velos Pro",
452+
name = "Orbitrap Velos Pro",
426453
cvRef = "MS",
427454
value = ""
428455
}
@@ -431,7 +458,7 @@ public static class OntologyMapping
431458
"ORBITRAP VELOS PRO", new CVParamType
432459
{
433460
accession = "MS:1003096",
434-
name = "LTQ Orbitrap Velos Pro",
461+
name = "Orbitrap Velos Pro",
435462
cvRef = "MS",
436463
value = ""
437464
}
@@ -440,7 +467,7 @@ public static class OntologyMapping
440467
"LTQ ORBITRAP ELITE", new CVParamType
441468
{
442469
accession = "MS:1001910",
443-
name = "LTQ Orbitrap Elite",
470+
name = "Orbitrap Elite",
444471
cvRef = "MS",
445472
value = ""
446473
}
@@ -449,7 +476,7 @@ public static class OntologyMapping
449476
"ORBITRAP ELITE", new CVParamType
450477
{
451478
accession = "MS:1001910",
452-
name = "LTQ Orbitrap Elite",
479+
name = "Orbitrap Elite",
453480
cvRef = "MS",
454481
value = ""
455482
}
@@ -508,11 +535,20 @@ public static class OntologyMapping
508535
value = ""
509536
}
510537
},
538+
{
539+
"VELOS PRO", new CVParamType
540+
{
541+
accession = "MS:1003495",
542+
name = "Velos Pro",
543+
cvRef = "MS",
544+
value = ""
545+
}
546+
},
511547
{
512548
"LTQ VELOS ETD", new CVParamType
513549
{
514550
accession = "MS:1000856",
515-
name = "LTQ Velos ETD",
551+
name = "LTQ Velos/ETD",
516552
cvRef = "MS",
517553
value = ""
518554
}
@@ -678,6 +714,69 @@ public static class OntologyMapping
678714
cvRef = "MS",
679715
value = ""
680716
}
717+
},
718+
{
719+
"TSQ QUANTUM ACCESS MAX", new CVParamType
720+
{
721+
accession = "MS:1003498",
722+
name = "TSQ Quantum Access MAX",
723+
cvRef = "MS",
724+
value = ""
725+
}
726+
},
727+
{
728+
"TSQ QUANTUM XLS", new CVParamType
729+
{
730+
accession = "MS:1003502",
731+
name = "TSQ Quantum XLS",
732+
cvRef = "MS",
733+
value = ""
734+
}
735+
},
736+
{
737+
"TSQ 8000", new CVParamType
738+
{
739+
accession = "MS:1003503",
740+
name = "TSQ 8000",
741+
cvRef = "MS",
742+
value = ""
743+
}
744+
},
745+
{
746+
"ISQ LT", new CVParamType
747+
{
748+
accession = "MS:1003500",
749+
name = "ISQ LT",
750+
cvRef = "MS",
751+
value = ""
752+
}
753+
},
754+
{
755+
"ITQ", new CVParamType
756+
{
757+
accession = "MS:1003501",
758+
name = "ITQ",
759+
cvRef = "MS",
760+
value = ""
761+
}
762+
},
763+
{
764+
"DELTAPLUS IRMS", new CVParamType
765+
{
766+
accession = "MS:1003504",
767+
name = "DeltaPlus IRMS",
768+
cvRef = "MS",
769+
value = ""
770+
}
771+
},
772+
{
773+
"THERMOQUEST VOYAGER", new CVParamType
774+
{
775+
accession = "MS:1003554",
776+
name = "ThermoQuest Voyager",
777+
cvRef = "MS",
778+
value = ""
779+
}
681780
}
682781
};
683782

@@ -776,8 +875,14 @@ public static List<CVParamType> GetDetectors(string instrumentAccession)
776875
case "MS:1000639":
777876
// MALDI LTQ ORBITRAP
778877
case "MS:1000643":
878+
// MALDI LTQ ORBITRAP XL
879+
case "MS:1003496":
880+
// MALDI LTQ ORBITRAP DISCOVERY
881+
case "MS:1003497":
779882
// LTQ ORBITRAP VELOS
780883
case "MS:1001742":
884+
// LTQ ORBITRAP VELOS/ETD
885+
case "MS:1003499":
781886
// LTQ ORBITRAP VELOS PRO
782887
case "MS:1003096":
783888
// LTQ ORBITRAP ELITE
@@ -812,6 +917,26 @@ public static List<CVParamType> GetDetectors(string instrumentAccession)
812917
}
813918
};
814919
break;
920+
// ORBITRAP ASTRAL
921+
case "MS:1003378":
922+
detectors = new List<CVParamType>
923+
{
924+
new CVParamType
925+
{
926+
accession = "MS:1000624",
927+
name = "inductive detector",
928+
cvRef = "MS",
929+
value = ""
930+
},
931+
new CVParamType
932+
{
933+
accession = "MS:1000108",
934+
name = "conversion dynode electron multiplier",
935+
cvRef = "MS",
936+
value = ""
937+
}
938+
};
939+
break;
815940
// EXACTIVE
816941
case "MS:1000649":
817942
// EXACTIVE PLUS
@@ -830,8 +955,6 @@ public static List<CVParamType> GetDetectors(string instrumentAccession)
830955
case "MS:1003094":
831956
// ORBITRAP EXPLORIS 480
832957
case "MS:1003028":
833-
// ORBITRAP ASTRAL
834-
case "MS:1003378":
835958
detectors = new List<CVParamType>
836959
{
837960
new CVParamType
@@ -847,6 +970,8 @@ public static List<CVParamType> GetDetectors(string instrumentAccession)
847970
case "MS:1000447":
848971
// LTQ VELOS
849972
case "MS:1000855":
973+
// VELOS PRO
974+
case "MS:1003495":
850975
// LTQ VELOS ETD
851976
case "MS:1000856":
852977
// LXQ
@@ -857,6 +982,18 @@ public static List<CVParamType> GetDetectors(string instrumentAccession)
857982
case "MS:1000638":
858983
// MALDI LTQ XL
859984
case "MS:1000642":
985+
// TSQ QUANTUM ACCESS MAX
986+
case "MS:1003498":
987+
// TSQ QUANTUM XLS
988+
case "MS:1003502":
989+
// TSQ 8000
990+
case "MS:1003503":
991+
// ISQ LT
992+
case "MS:1003500":
993+
// ITQ
994+
case "MS:1003501":
995+
// THERMOQUEST VOYAGER
996+
case "MS:1003554":
860997
detectors = new List<CVParamType>
861998
{
862999
new CVParamType
@@ -868,6 +1005,19 @@ public static List<CVParamType> GetDetectors(string instrumentAccession)
8681005
}
8691006
};
8701007
break;
1008+
// DELTAPLUS IRMS
1009+
case "MS:1003504":
1010+
detectors = new List<CVParamType>
1011+
{
1012+
new CVParamType
1013+
{
1014+
accession = "MS:1000112",
1015+
name = "faraday cup",
1016+
cvRef = "MS",
1017+
value = ""
1018+
}
1019+
};
1020+
break;
8711021
default:
8721022
detectors = new List<CVParamType>
8731023
{

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